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- PDB-3b9n: Crystal structure of long-chain alkane monooxygenase (LadA) -

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Basic information

Entry
Database: PDB / ID: 3b9n
TitleCrystal structure of long-chain alkane monooxygenase (LadA)
ComponentsAlkane monooxygenase
KeywordsOXIDOREDUCTASE / Geobacillus thermodenitrificans / LADA / ALKANE HYDROXYLASE / MONOOXYGENASE / Plasmid
Function / homology
Function and homology information


long-chain alkane monooxygenase / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / nucleotide binding / extracellular region
Similarity search - Function
Nitrilotriacetate monooxygenase component A/pristinamycin IIA synthase subunit A / : / Luciferase-like domain / Luciferase-like domain / Luciferase-like monooxygenase / Luciferase-like domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Long-chain alkane monooxygenase
Similarity search - Component
Biological speciesGeobacillus thermodenitrificans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsLi, L. / Yang, W. / Xu, F. / Bartlam, M. / Rao, Z.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Crystal structure of long-chain alkane monooxygenase (LadA) in complex with coenzyme FMN: unveiling the long-chain alkane hydroxylase
Authors: Li, L. / Liu, X. / Yang, W. / Xu, F. / Wang, W. / Feng, L. / Bartlam, M. / Wang, L. / Rao, Z.
History
DepositionNov 6, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alkane monooxygenase
B: Alkane monooxygenase


Theoretical massNumber of molelcules
Total (without water)101,0802
Polymers101,0802
Non-polymers00
Water6,053336
1
A: Alkane monooxygenase


Theoretical massNumber of molelcules
Total (without water)50,5401
Polymers50,5401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Alkane monooxygenase


Theoretical massNumber of molelcules
Total (without water)50,5401
Polymers50,5401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.502, 77.502, 323.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Alkane monooxygenase


Mass: 50540.121 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus thermodenitrificans (bacteria)
Gene: ladA / Plasmid: PET28A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): bl21
References: UniProt: A4IU28, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With reduced iron-sulfur protein as one donor, and incorporation of one ...References: UniProt: A4IU28, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With reduced iron-sulfur protein as one donor, and incorporation of one atom of oxygen into the other donor
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 336 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.85 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2-0.3M potassium sodium tartrate tetrahydrate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 25, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 28293 / % possible obs: 0.95 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.06
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.06 / Mean I/σ(I) obs: 13.1 / % possible all: 0.95

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TVL

1tvl


Resolution: 2.7→50 Å / Cross valid method: THROUGHOUT
RfactorNum. reflectionSelection details
Rfree0.249 1999 RANDOM
Rwork0.183 --
all-28293 -
obs-20382 -
Refinement stepCycle: LAST / Resolution: 2.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7033 0 0 336 7369
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.307
X-RAY DIFFRACTIONc_bond_d0.006

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